#include "potentials/tersoff.h"
#endif
-/* pse */
-#define PSE_MASS
-#include "pse.h"
-#undef PSE_MASS
-
#define ME "[mdrun]"
/*
case STAGE_DISPLACE_ATOM:
psize=sizeof(t_displace_atom_params);
break;
+ case STAGE_DEL_ATOMS:
+ psize=sizeof(t_del_atoms_params);
+ break;
+ case STAGE_MODIFY_ATOMS:
+ psize=sizeof(t_modify_atoms_params);
+ break;
case STAGE_INSERT_ATOMS:
psize=sizeof(t_insert_atoms_params);
break;
case STAGE_SET_TIMESTEP:
psize=sizeof(t_set_timestep_params);
break;
+ case STAGE_FILL:
+ psize=sizeof(t_fill_params);
+ break;
+ case STAGE_THERMAL_INIT:
+ psize=0;
+ break;
default:
printf("%s unknown stage type: %02x\n",ME,type);
return -1;
char error[128];
char line[128];
char *wptr;
- char word[16][64];
+ char word[32][64];
int wcnt;
int i,o;
t_displace_atom_params dap;
+ t_modify_atoms_params map;
t_insert_atoms_params iap;
t_insert_mixed_atoms_params imp;
t_continue_params cp;
t_chsattr_params csp;
t_set_temp_params stp;
t_set_timestep_params stsp;
+ t_fill_params fp;
+ t_del_atoms_params delp;
/* open config file */
fd=open(mdrun->cfile,O_RDONLY);
// reset
memset(&iap,0,sizeof(t_insert_atoms_params));
+ memset(&map,0,sizeof(t_modify_atoms_params));
memset(&imp,0,sizeof(t_insert_mixed_atoms_params));
memset(&cp,0,sizeof(t_continue_params));
memset(&ap,0,sizeof(t_anneal_params));
memset(&csp,0,sizeof(t_chsattr_params));
memset(&stp,0,sizeof(t_set_temp_params));
memset(&stsp,0,sizeof(t_set_timestep_params));
+ memset(&fp,0,sizeof(t_fill_params));
+ memset(&delp,0,sizeof(t_del_atoms_params));
// get command + args
wcnt=0;
mdrun->lattice=DIAMOND;
if(!strncmp(word[1],"none",4))
mdrun->lattice=NONE;
+ if(wcnt==3)
+ mdrun->lc=atof(word[2]);
}
else if(!strncmp(word[0],"element1",8)) {
mdrun->element1=atoi(word[1]);
- mdrun->m1=pse_mass[mdrun->element1];
}
else if(!strncmp(word[0],"element2",8)) {
mdrun->element2=atoi(word[1]);
- mdrun->m2=pse_mass[mdrun->element2];
}
else if(!strncmp(word[0],"fill",6)) {
- // only lc mode by now
- mdrun->lx=atoi(word[2]);
- mdrun->ly=atoi(word[3]);
- mdrun->lz=atoi(word[4]);
- mdrun->lc=atof(word[5]);
- if(wcnt==8) {
- mdrun->fill_element=atoi(word[6]);
- mdrun->fill_brand=atoi(word[7]);
- }
- else {
- mdrun->fill_element=mdrun->element1;
- mdrun->fill_brand=0;
+ // default values
+ fp.fill_element=mdrun->element1;
+ fp.fill_brand=0;
+ fp.lattice=mdrun->lattice;
+ fp.p_params.type=0;
+ fp.d_params.type=0;
+ fp.d_params.stype=0;
+ // parse fill command
+ i=1;
+ while(i<wcnt) {
+ if(!strncmp(word[i],"lc",2)) {
+ fp.lx=atoi(word[++i]);
+ fp.ly=atoi(word[++i]);
+ fp.lz=atoi(word[++i]);
+ fp.lc=atof(word[++i]);
+ mdrun->lc=fp.lc;
+ continue;
+ }
+ if(!strncmp(word[i],"eb",2)) {
+ fp.fill_element=atoi(word[++i]);
+ fp.fill_brand=atoi(word[++i]);
+ continue;
+ }
+ if(word[i][0]=='p') {
+ i+=1;
+ switch(word[i][0]) {
+ case 'i':
+ if(word[i][1]=='r')
+ fp.p_params.type=PART_INSIDE_R;
+ else
+ fp.p_params.type=PART_INSIDE_D;
+ break;
+ case 'o':
+ if(word[i][1]=='r')
+ fp.p_params.type=PART_OUTSIDE_R;
+ else
+ fp.p_params.type=PART_OUTSIDE_D;
+ break;
+ default:
+ break;
+ }
+ if((fp.p_params.type==PART_INSIDE_R)||
+ (fp.p_params.type==PART_OUTSIDE_R)) {
+ fp.p_params.r=atof(word[++i]);
+ fp.p_params.p.x=atof(word[++i]);
+ fp.p_params.p.y=atof(word[++i]);
+ fp.p_params.p.z=atof(word[++i]);
+ }
+ if((fp.p_params.type==PART_INSIDE_D)||
+ (fp.p_params.type==PART_OUTSIDE_D)) {
+ fp.p_params.p.x=atof(word[++i]);
+ fp.p_params.p.y=atof(word[++i]);
+ fp.p_params.p.z=atof(word[++i]);
+ fp.p_params.d.x=atof(word[++i]);
+ fp.p_params.d.y=atof(word[++i]);
+ fp.p_params.d.z=atof(word[++i]);
+ }
+ continue;
+ }
+ if(word[i][0]=='d') {
+ switch(word[++i][0]) {
+ case '0':
+
+ fp.d_params.type=DEFECT_TYPE_0D;
+ if(!strncmp(word[i+1],"dbx",3)) {
+ fp.d_params.stype=DEFECT_STYPE_DB_X;
+ }
+ if(!strncmp(word[i+1],"dby",3)) {
+ fp.d_params.stype=DEFECT_STYPE_DB_Y;
+ }
+ if(!strncmp(word[i+1],"dbz",3)) {
+ fp.d_params.stype=DEFECT_STYPE_DB_Z;
+ }
+ if(!strncmp(word[i+1],"dbr",3)) {
+ fp.d_params.stype=DEFECT_STYPE_DB_R;
+ }
+ i+=1;
+ fp.d_params.od=atof(word[++i]);
+ fp.d_params.dd=atof(word[++i]);
+ fp.d_params.element=atoi(word[++i]);
+ fp.d_params.brand=atoi(word[++i]);
+ // parsed in future
+ fp.d_params.attr=ATOM_ATTR_HB|ATOM_ATTR_VA;
+ fp.d_params.attr|=ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP;
+ break;
+
+ case '1':
+ fp.d_params.type=DEFECT_TYPE_1D;
+ break;
+ case '2':
+ fp.d_params.type=DEFECT_TYPE_2D;
+ break;
+ case '3':
+ fp.d_params.type=DEFECT_TYPE_3D;
+ break;
+ default:
+ break;
+ }
+ continue;
+
+ }
+ i+=1;
}
+ add_stage(mdrun,STAGE_FILL,&fp);
+ }
+ else if(!strncmp(word[0],"thermal_init",12)) {
+ add_stage(mdrun,STAGE_THERMAL_INIT,NULL);
}
else if(!strncmp(word[0],"aattr",5)) {
// for aatrib line we need a special stage
}
i=2;
if(cap.type&CHAATTR_REGION) {
- cap.x0=atof(word[1]);
- cap.y0=atof(word[2]);
- cap.z0=atof(word[3]);
- cap.x1=atof(word[4]);
- cap.y1=atof(word[5]);
- cap.z1=atof(word[6]);
+ cap.x0=atof(word[2]);
+ cap.y0=atof(word[3]);
+ cap.z0=atof(word[4]);
+ cap.x1=atof(word[5]);
+ cap.y1=atof(word[6]);
+ cap.z1=atof(word[7]);
i+=6;
}
if(cap.type&CHAATTR_ELEMENT) {
csp.type=0;
for(i=1;i<wcnt;i++) {
if(!strncmp(word[i],"pctrl",5)) {
- csp.ptau=0.01/(atof(word[++i])*GPA);
+ csp.ptau=atof(word[++i]);
+ if(csp.ptau>0)
+ csp.ptau=0.01/(csp.ptau*GPA);
csp.type|=CHSATTR_PCTRL;
}
if(!strncmp(word[i],"tctrl",5)) {
dap.dz=atof(word[5]);
add_stage(mdrun,STAGE_DISPLACE_ATOM,&dap);
}
+ else if(!strncmp(word[1],"del_atoms",9)) {
+ delp.o.x=atof(word[2]);
+ delp.o.y=atof(word[3]);
+ delp.o.z=atof(word[4]);
+ delp.r=atof(word[5]);
+ add_stage(mdrun,STAGE_DEL_ATOMS,&delp);
+ }
+ else if(!strncmp(word[1],"mod_atoms",8)) {
+ i=2;
+ while(i<wcnt) {
+ if(!strncmp(word[i],"t",1)) {
+ map.tag=atoi(word[++i]);
+ i+=1;
+ }
+ if(!strncmp(word[i],"ekin",5)) {
+ map.ekin.x=atof(word[++i])*EV;
+ map.ekin.y=atof(word[++i])*EV;
+ map.ekin.z=atof(word[++i])*EV;
+ i+=1;
+ }
+ }
+ add_stage(mdrun,STAGE_MODIFY_ATOMS,&map);
+ }
else if(!strncmp(word[1],"ins_atoms",9)) {
iap.ins_steps=atoi(word[2]);
iap.ins_atoms=atoi(word[3]);
iap.z0=atof(word[10]);
break;
case 'r':
- if(word[8][0]=='t') {
+ switch(word[8][0]) {
+
+ case 't':
iap.type=INS_TOTAL;
iap.cr=atof(word[9]);
- }
- else {
- iap.type=INS_REGION;
- iap.x0=atof(word[8]);
- iap.y0=atof(word[9]);
- iap.z0=atof(word[10]);
- iap.x1=atof(word[11]);
- iap.y1=atof(word[12]);
- iap.z1=atof(word[13]);
- iap.cr=atof(word[14]);
+ break;
+ case 'r':
+ iap.type=INS_RECT;
+ iap.x0=atof(word[9]);
+ iap.y0=atof(word[10]);
+ iap.z0=atof(word[11]);
+ iap.x1=atof(word[12]);
+ iap.y1=atof(word[13]);
+ iap.z1=atof(word[14]);
+ iap.cr=atof(word[15]);
+ break;
+ case 's':
+ iap.type=INS_SPHERE;
+ iap.x0=atof(word[9]);
+ iap.y0=atof(word[10]);
+ iap.z0=atof(word[11]);
+ iap.x1=atof(word[12]);
+ iap.cr=atof(word[13]);
+ break;
+ default:
+ break;
}
default:
break;
return 0;
}
+int del_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
+
+ t_stage *stage;
+ t_del_atoms_params *delp;
+ int i;
+ t_3dvec dist;
+
+ stage=mdrun->stage.current->data;
+ delp=stage->params;
+
+ for(i=0;i<moldyn->count;i++) {
+ v3_sub(&dist,&(delp->o),&(moldyn->atom[i].r));
+//printf("%d ----> %f %f %f = %f | %f\n",i,dist.x,dist.y,dist.z,v3_absolute_square(&dist),delp->r*delp->r);
+ if(v3_absolute_square(&dist)<=(delp->r*delp->r)) {
+ del_atom(moldyn,moldyn->atom[i].tag);
+ printf("%s atom deleted: %d %d %d\n",ME,
+ moldyn->atom[i].tag,moldyn->atom[i].element,
+ moldyn->atom[i].brand);
+ }
+ }
+
+ return 0;
+}
+
+int modify_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
+
+ t_modify_atoms_params *map;
+ t_stage *stage;
+ t_atom *atom;
+ t_3dvec v;
+ int i;
+
+ atom=moldyn->atom;
+ stage=mdrun->stage.current->data;
+ map=stage->params;
+ v.x=0.0; v.y=0.0; v.z=0.0;
+
+ for(i=0;i<moldyn->count;i++) {
+ if(atom[i].tag==map->tag) {
+ v.x=sqrt(2.0*fabs(map->ekin.x)/atom[i].mass);
+ if(map->ekin.x<0.0)
+ v.x=-v.x;
+ v.y=sqrt(2.0*fabs(map->ekin.y)/atom[i].mass);
+ if(map->ekin.y<0.0)
+ v.y=-v.y;
+ v.z=sqrt(2.0*fabs(map->ekin.z)/atom[i].mass);
+ if(map->ekin.z<0.0)
+ v.z=-v.z;
+ v3_copy(&(atom[i].v),&v);
+ printf("%s atom modified: v = (%f %f %f)\n",
+ ME,v.x,v.y,v.z);
+ }
+ }
+
+ return 0;
+}
+
int insert_atoms(t_moldyn *moldyn,t_mdrun *mdrun) {
t_insert_atoms_params *iap;
z0=-z/2.0;
cr_check=TRUE;
break;
- case INS_REGION:
+ case INS_RECT:
x=iap->x1-iap->x0;
x0=iap->x0;
y=iap->y1-iap->y0;
z0=iap->z0;
cr_check=TRUE;
break;
+ case INS_SPHERE:
+ x=2.0*iap->x1;
+ x0=iap->x0-iap->x1;
+ y=x;
+ y0=iap->y0-iap->x1;
+ z=x;
+ z0=iap->z0-iap->x1;
+ cr_check=TRUE;
+ break;
case INS_POS:
x0=iap->x0;
y0=iap->y0;
dmin=d;
}
}
+ if(iap->type==INS_SPHERE) {
+ if((r.x-iap->x0)*(r.x-iap->x0)+
+ (r.y-iap->y0)*(r.y-iap->y0)+
+ (r.z-iap->z0)*(r.z-iap->z0)>
+ (iap->x1*iap->x1)) {
+ run=1;
+ }
+ }
}
- add_atom(moldyn,iap->element,pse_mass[iap->element],
+ add_atom(moldyn,iap->element,
iap->brand,iap->attr,&r,&v);
printf("%s atom inserted (%d/%d): %f %f %f\n",
ME,(iap->cnt_steps+1)*iap->ins_atoms,
iap->ins_steps*iap->ins_atoms,r.x,r.y,r.z);
- printf(" -> d2 = %f/%f\n",dmin,iap->cr*iap->cr);
+ printf(" attributes: ");
+ if(iap->attr&ATOM_ATTR_VB)
+ printf("b ");
+ if(iap->attr&ATOM_ATTR_HB)
+ printf("h ");
+ if(iap->attr&ATOM_ATTR_VA)
+ printf("v ");
+ if(iap->attr&ATOM_ATTR_FP)
+ printf("f ");
+ if(iap->attr&ATOM_ATTR_1BP)
+ printf("1 ");
+ if(iap->attr&ATOM_ATTR_2BP)
+ printf("2 ");
+ if(iap->attr&ATOM_ATTR_3BP)
+ printf("3 ");
+ printf("\n");
+ printf(" d2 = %f/%f\n",dmin,iap->cr*iap->cr);
cnt+=1;
}
if(dmin>cmax)
retry=1;
}
- add_atom(moldyn,imp->element1,pse_mass[imp->element1],
+ add_atom(moldyn,imp->element1,
imp->brand1,imp->attr1,&r,&v);
printf("%s (mixed) atom inserted (%d): %f %f %f\n",
ME,imp->amount1,r.x,r.y,r.z);
if(dmin>cmax)
retry=1;
}
- add_atom(moldyn,imp->element2,pse_mass[imp->element2],
+ add_atom(moldyn,imp->element2,
imp->brand2,imp->attr2,&r,&v);
printf("%s (mixed) atom inserted (%d): %f %f %f\n",
ME,imp->amount2,r.x,r.y,r.z);
continue;
}
if(cap->type&CHAATTR_REGION) {
- if(cap->x0<atom->r.x)
+ if(cap->x0>atom->r.x)
continue;
- if(cap->y0<atom->r.y)
+ if(cap->y0>atom->r.y)
continue;
- if(cap->z0<atom->r.z)
+ if(cap->z0>atom->r.z)
continue;
- if(cap->x1>atom->r.x)
+ if(cap->x1<atom->r.x)
continue;
- if(cap->y1>atom->r.y)
+ if(cap->y1<atom->r.y)
continue;
- if(cap->z1>atom->r.z)
+ if(cap->z1<atom->r.z)
continue;
}
+ printf(" changing attributes of atom %d (0x%x)\n",i,cap->attr);
atom->attr=cap->attr;
}
+ printf("\n\n");
+
return 0;
}
if(csp->ptau>0)
set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
else
- set_p_scale(moldyn,P_SCALE_BERENDSEN,csp->ptau);
+ set_p_scale(moldyn,P_SCALE_NONE,1.0);
}
if(csp->type&CHSATTR_TCTRL) {
if(csp->ttau>0)
set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
else
- set_t_scale(moldyn,T_SCALE_BERENDSEN,csp->ttau);
+ set_t_scale(moldyn,T_SCALE_NONE,1.0);
}
if(csp->type&CHSATTR_PRELAX) {
if(csp->dp<0)
t_list *sl;
int steps;
u8 change_stage;
+ t_3dvec o;
t_insert_atoms_params *iap;
t_insert_mixed_atoms_params *imp;
t_anneal_params *ap;
t_set_temp_params *stp;
t_set_timestep_params *stsp;
+ t_fill_params *fp;
moldyn=ptr1;
mdrun=ptr2;
displace_atom(moldyn,mdrun);
change_stage=TRUE;
break;
+ case STAGE_DEL_ATOMS:
+ stage_print(" -> del atoms\n\n");
+ del_atoms(moldyn,mdrun);
+ change_stage=TRUE;
+ break;
+ case STAGE_MODIFY_ATOMS:
+ stage_print(" -> modify atoms\n\n");
+ modify_atoms(moldyn,mdrun);
+ change_stage=TRUE;
+ break;
case STAGE_INSERT_ATOMS:
stage_print(" -> insert atoms\n\n");
iap=stage->params;
mdrun->timestep=stsp->tau;
change_stage=TRUE;
break;
+ case STAGE_FILL:
+ stage_print(" -> fill lattice\n\n");
+ fp=stage->params;
+ switch(fp->lattice) {
+ case ZINCBLENDE:
+
+ o.x=0.5*0.25*fp->lc;
+ o.y=o.x;
+ o.z=o.x;
+ create_lattice(moldyn,
+ FCC,fp->lc,
+ mdrun->element1,
+ DEFAULT_ATOM_ATTR,0,
+ fp->lx,fp->ly,fp->lz,
+ &o,
+ &(fp->p_params),
+ &(fp->d_params));
+ o.x+=0.25*fp->lc;
+ o.y=o.x;
+ o.z=o.x;
+ create_lattice(moldyn,
+ FCC,fp->lc,
+ mdrun->element2,
+ DEFAULT_ATOM_ATTR,1,
+ fp->lx,fp->ly,fp->lz,
+ &o,
+ &(fp->p_params),
+ &(fp->d_params));
+ break;
+
+ default:
+
+ create_lattice(moldyn,
+ fp->lattice,fp->lc,
+ fp->fill_element,
+ DEFAULT_ATOM_ATTR,
+ fp->fill_brand,
+ fp->lx,fp->ly,fp->lz,
+ NULL,
+ &(fp->p_params),
+ &(fp->d_params));
+ break;
+ }
+ moldyn_bc_check(moldyn);
+ change_stage=TRUE;
+ break;
+ case STAGE_THERMAL_INIT:
+ stage_print(" -> thermal init\n\n");
+ thermal_init(moldyn,TRUE);
+ change_stage=TRUE;
+ break;
default:
printf("%s unknwon stage type\n",ME);
break;
t_mdrun mdrun;
t_moldyn moldyn;
- t_3dvec o;
+ //t_3dvec o;
/* clear structs */
memset(&mdrun,0,sizeof(t_mdrun));
/* initial lattice and dimensions */
set_dim(&moldyn,mdrun.dim.x,mdrun.dim.y,mdrun.dim.z,mdrun.vis);
set_pbc(&moldyn,mdrun.pbcx,mdrun.pbcy,mdrun.pbcz);
+ /* replaced by fill stage !!
switch(mdrun.lattice) {
case FCC:
create_lattice(&moldyn,FCC,mdrun.lc,mdrun.fill_element,
mdrun.m1,DEFAULT_ATOM_ATTR,
mdrun.fill_brand,mdrun.lx,
- mdrun.ly,mdrun.lz,NULL);
+ mdrun.ly,mdrun.lz,NULL,0,NULL);
break;
case DIAMOND:
create_lattice(&moldyn,DIAMOND,mdrun.lc,
mdrun.fill_element,
mdrun.m1,DEFAULT_ATOM_ATTR,
mdrun.fill_brand,mdrun.lx,
- mdrun.ly,mdrun.lz,NULL);
+ mdrun.ly,mdrun.lz,NULL,0,NULL);
break;
case ZINCBLENDE:
o.x=0.5*0.25*mdrun.lc; o.y=o.x; o.z=o.x;
create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element1,
mdrun.m1,DEFAULT_ATOM_ATTR,0,mdrun.lx,
- mdrun.ly,mdrun.lz,&o);
+ mdrun.ly,mdrun.lz,&o,0,NULL);
o.x+=0.25*mdrun.lc; o.y=o.x; o.z=o.x;
create_lattice(&moldyn,FCC,mdrun.lc,mdrun.element2,
mdrun.m2,DEFAULT_ATOM_ATTR,1,mdrun.lx,
- mdrun.ly,mdrun.lz,&o);
+ mdrun.ly,mdrun.lz,&o,0,NULL);
break;
case NONE:
set_nn_dist(&moldyn,mdrun.nnd);
return -1;
}
moldyn_bc_check(&moldyn);
+ replaced by fill stage !! */
/* temperature and pressure */
set_temperature(&moldyn,mdrun.temperature);
set_pressure(&moldyn,mdrun.pressure);
+ /* replaced thermal_init stage
thermal_init(&moldyn,TRUE);
+ */
addsched:
/* first schedule */